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- PDB-5lw2: Crystal structure of DARPin 5m3_D12 -

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Basic information

Entry
Database: PDB / ID: 5lw2
TitleCrystal structure of DARPin 5m3_D12
ComponentsDARPin_5m3_D12
KeywordsDE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / ACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBatyuk, A. / Wu, Y. / Plueckthun, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_166676 Switzerland
European Research CouncilNEXTBINDERS
CitationJournal: Sci Rep / Year: 2017
Title: Rigidly connected multispecific artificial binders with adjustable geometries.
Authors: Wu, Y. / Batyuk, A. / Honegger, A. / Brandl, F. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionSep 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DARPin_5m3_D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2533
Polymers18,1351
Non-polymers1182
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-0 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.130, 28.000, 52.730
Angle α, β, γ (deg.)90.00, 104.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DARPin_5m3_D12


Mass: 18135.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 1000 10% PEG 8000 10% Ca-acetate 0.2 M Tris(HOAc) 0.1 M pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.75→46.527 Å / Num. obs: 14009 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1054 / Net I/σ(I): 8.85
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.654 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.529 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 1.75→46.527 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.38
RfactorNum. reflection% reflection
Rfree0.2608 699 5.01 %
Rwork0.2205 --
obs0.2225 13948 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→46.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 8 93 1264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031186
X-RAY DIFFRACTIONf_angle_d0.4521611
X-RAY DIFFRACTIONf_dihedral_angle_d9.598699
X-RAY DIFFRACTIONf_chiral_restr0.036190
X-RAY DIFFRACTIONf_plane_restr0.002215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.88520.43891380.38742596X-RAY DIFFRACTION99
1.8852-2.07490.39841370.29492616X-RAY DIFFRACTION99
2.0749-2.37510.29481400.25232647X-RAY DIFFRACTION100
2.3751-2.99230.26091390.2182650X-RAY DIFFRACTION100
2.9923-46.54350.20971450.18222740X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6254-1.2655-1.76463.02241.05286.6713-0.15620.4342-0.1528-0.27480.03050.36170.0024-0.7110.10450.2417-0.0624-0.00880.2602-0.01160.25-36.9832-4.640515.4087
24.2852-1.6663-2.64494.10490.55254.6339-0.19430.3838-0.05180.07890.06230.18290.28670.15450.08880.2344-0.051-0.02170.2118-0.00850.1879-26.4009-8.56714.8221
35.28952.7817-2.79794.008-2.52281.9070.01-0.1830.68620.38010.0417-0.3601-1.12821.29870.36450.3393-0.1728-0.01620.3562-0.04060.3097-18.5983-3.86519.4343
42.561-0.7444-0.44790.963-0.74234.94210.0040.7275-0.03470.039-0.2067-0.03990.43611.21680.09610.27810.0178-0.00420.5521-0.00580.2547-16.8243-11.98168.3929
53.39470.13910.80741.21530.57615.52910.09520.310.12960.1127-0.1139-0.08650.47081.80720.04770.25440.074-0.02670.81160.04380.3041-10.305-12.87349.211
67.1972-1.61523.90419.56645.396.4310.56340.16870.7277-1.20450.2864-0.4457-1.56061.4007-0.45880.70390.15270.23151.23520.03820.5725-4.679-9.4992.4678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 167 )

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